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Recent advances in optical-based and force-based single nucleic acid imaging

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Abstract

The capability to image, as well as control and manipulate single molecules such as nucleic acids (DNA or RNA) can greatly enrich our knowledge of the roles of individual biomolecules in cellular processes and their behavior in native environments. Here we summarize the recent advances of single nucleic acid imaging based on optical observation and force manipulation. We start by discussing the superiority of single molecule image, the central roles nucleic acids play in biosystems, and the significance of single molecule image towards nucleic acids. We then list a series of representative examples in brief to illustrate how nucleic acid of various morphologies has been imaged from different aspects, and what can be learned from such characterizations. Finally, concluding remarks on parts of which should be improved and outlook are outlined.

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References

  1. Cordova JC, Das DK, Manning HW, Lang MJ. Curr Opin Struct Biol, 2014, 28: 142–148

    Article  CAS  Google Scholar 

  2. Binnig G, Quate CF, Gerber C. Phys Rev Lett, 1986, 56: 930–933

    Article  CAS  Google Scholar 

  3. Binnig G, Rohrer H. Rev Mod Phys, 1987, 59: 615–625

    Article  CAS  Google Scholar 

  4. Zhang M, He K, Wu J, Li N, Yuan J, Zhou W, Ye Z, Li Z, Xiao H, Lv Z, Zhang Y, Fang X. Sci China Chem, 2017, 275: doi: 10.1007/s11426-017-9072-5

    Google Scholar 

  5. Willets KA, Ostroverkhova O, He M, Twieg RJ, Moerner WE. J Am Chem Soc, 2003, 125: 1174–1175

    Article  CAS  Google Scholar 

  6. Gordon MP, Ha T, Selvin PR. Proc Natl Acad Sci USA, 2004, 101: 6462–6465

    Article  CAS  Google Scholar 

  7. Stroh C, Wang H, Bash R, Ashcroft B, Nelson J, Gruber H, Lohr D, Lindsay SM, Hinterdorfer P. Proc Natl Acad Sci USA, 2004, 101: 12503–12507

    Article  CAS  Google Scholar 

  8. Rasnik I, McKinney SA, Ha T. Nat Meth, 2006, 3: 891–893

    Article  CAS  Google Scholar 

  9. Finkelstein IJ, Visnapuu ML, Greene EC. Nature, 2010, 468: 983–987

    Article  CAS  Google Scholar 

  10. Gu JY, Cai ZF, Wang D, Wan LJ. ACS Nano, 2016, 10: 8746–8750

    Article  CAS  Google Scholar 

  11. Arroyo JO, Kukura P. Nat Photon, 2015, 10: 11–17

    Article  Google Scholar 

  12. Moerner WE, Orrit M, Wild UP, Basché T. Single-molecule Optical Detection, Imaging and Spectroscopy. New York: John Wiley & Sons, 2008

    Google Scholar 

  13. Walter NG, Bustamante C. Chem Rev, 2014, 114: 3069–3071

    Article  CAS  Google Scholar 

  14. Duzdevich D, Redding S, Greene EC. Chem Rev, 2014, 114: 3072–3086

    Article  CAS  Google Scholar 

  15. Gan JH, Sheng J, Huang Z. Sci China Chem, 2011, 54: 3–23

    Article  CAS  Google Scholar 

  16. Min X, Zhang M, Huang F, Lou X, Xia F. ACS Appl Mater Interfaces, 2016, 8: 8998–9003

    Article  CAS  Google Scholar 

  17. Morikawa K, Yanagida M. J Biochem, 1981, 89: 693–696

    Article  CAS  Google Scholar 

  18. Houseal TW, Bustamante C, Stump RF, Maestre MF. BioPhys J, 1989, 56: 507–516

    Article  CAS  Google Scholar 

  19. Beebe TP, Wilson TE, Ogletree DF, Katz JE, Balhorn R, Salmeron MB, Siekhaus WJ. Science, 1989, 243: 370–372

    Article  CAS  Google Scholar 

  20. Keller D, Bustamante C, Keller RW. Proc Natl Acad Sci USA, 1989, 86: 5356–5360

    Article  CAS  Google Scholar 

  21. Veigel C, Schmidt CF. Nat Rev Mol Cell Biol, 2011, 12: 163–176

    Article  CAS  Google Scholar 

  22. Finkelstein IJ, Greene EC. DNA Recombination: Methods and Protocols. Totowa: Humana Press, 2011. 447–461

    Book  Google Scholar 

  23. Moerner WE. Proc Natl Acad Sci USA, 2007, 104: 12596–12602

    Article  CAS  Google Scholar 

  24. Xia T, Li N, Fang X. Annu Rev Phys Chem, 2013, 64: 459–480

    Article  CAS  Google Scholar 

  25. Hohng S, Lee S, Lee J, Jo MH. Chem Soc Rev, 2014, 43: 1007–1013

    Article  CAS  Google Scholar 

  26. Kozankiewicz B, Orrit M. Chem Soc Rev, 2014, 43: 1029–1043

    Article  CAS  Google Scholar 

  27. Bustamante C, Cheng W, Mejia YX, Meija YX. Cell, 2011, 144: 480–497

    Article  CAS  Google Scholar 

  28. Kemmerich FE, Swoboda M, Kauert DJ, Grieb MS, Hahn S, Schwarz FW, Seidel R, Schlierf M. Nano Lett, 2016, 16: 381–386

    Article  CAS  Google Scholar 

  29. Lyubchenko YL. Cell Biochem Biophys, 2004, 41: 075–098

    Article  CAS  Google Scholar 

  30. Miller H, Zhou Z, Wollman AJM, Leake MC. Methods, 2015, 88: 81–88

    Article  CAS  Google Scholar 

  31. Backer AS, Lee MY, Moerner WE. Optica, 2016, 3: 659–666

    Article  CAS  Google Scholar 

  32. Backlund MP, Arbabi A, Petrov PN, Arbabi E, Saurabh S, Faraon A, Moerner WE. Nat Photon, 2016, 10: 459–462

    Article  CAS  Google Scholar 

  33. Contreras-Naranjo JC, Wei Q, Ozcan A. IEEE J Sel Top, Quantum Electron, 2016, 22: 392–405

    Article  Google Scholar 

  34. Wei Q, Luo W, Chiang S, Kappel T, Mejia C, Tseng D, Chan RYL, Yan E, Qi H, Shabbir F, Ozkan H, Feng S, Ozcan A. ACS Nano, 2014, 8: 12725–12733

    Article  CAS  Google Scholar 

  35. Kühnemund M, Wei Q, Darai E, Wang Y, Hernández-Neuta I, Yang Z, Tseng D, Ahlford A, Mathot L, Sjöblom T, Ozcan A, Nilsson M. Nat Commun, 2017, 8: 13913

    Article  Google Scholar 

  36. Ma F, Li Y, Tang B, Zhang CY. Acc Chem Res, 2016, 49: 1722–1730

    Article  CAS  Google Scholar 

  37. Ha T, Tinnefeld P. Annu Rev Phys Chem, 2012, 63: 595–617

    Article  CAS  Google Scholar 

  38. Yu H, Shan X, Wang S, Chen H, Tao N. ACS Nano, 2014, 8: 3427–3433

    Article  CAS  Google Scholar 

  39. Dinish US, Song Z, Ho CJH, Balasundaram G, Attia ABE, Lu X, Tang BZ, Liu B, Olivo M. Adv Funct Mater, 2015, 25: 2316–2325

    Article  CAS  Google Scholar 

  40. Neuman KC, Nagy A. Nat Meth, 2008, 5: 491–505

    Article  CAS  Google Scholar 

  41. Shiotari A, Sugimoto Y. Nat Commun, 2017, 8: 14313

    Article  CAS  Google Scholar 

  42. Kim S, Blainey PC, Schroeder CM, Xie XS. Nat Meth, 2007, 40: 397–399

    CAS  Google Scholar 

  43. Footer MJ, Kerssemakers JWJ, Theriot JA, Dogterom M. Proc Natl Acad Sci USA, 2007, 104: 2181–2186

    Article  CAS  Google Scholar 

  44. Bezrukavnikov S, Mashaghi A, van Wijk RJ, Gu C, Yang LJ, Gao YQ, Tans SJ. Soft Matter, 2014, 10: 7269–7277

    Article  CAS  Google Scholar 

  45. Heller I, Laurens N, Vorselen D, Broekmans OD, Biebricher AS, King GA, Brouwer I, Wuite GJL, Peterman EJG. Optical Tweezers: Methods and Protocols. New York: Springer New York, 2017. 257–272

    Book  Google Scholar 

  46. De Vlaminck I, Dekker C. Annu Rev Biophys, 2012, 41: 453–472

    Article  Google Scholar 

  47. Sarkar R, Rybenkov VV. Front Phys, 2016, 4: 48

    Article  Google Scholar 

  48. Kriegel F, Ermann N, Lipfert J. J Struct Biol, 2017, 197: 26–36

    Article  CAS  Google Scholar 

  49. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F. Science, 1996, 271: 792–794

    Article  CAS  Google Scholar 

  50. Evans E, Ritchie K, Merkel R. BioPhys J, 1995, 68: 2580–2587

    Article  CAS  Google Scholar 

  51. Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Annu Rev Biochem, 2016, 85: 349–373

    Article  CAS  Google Scholar 

  52. Endo M, Sugiyama H. Acc Chem Res, 2014, 47: 1645–1653

    Article  CAS  Google Scholar 

  53. Gu H. Sci China Chem, 2017, 60, doi: 10.1007/s11426-017-9073-6

    Google Scholar 

  54. Alonso-Sarduy L, Longo G, Dietler G, Kasas S. Nano Lett, 2013, 13: 5679–5684

    Article  CAS  Google Scholar 

  55. Quigley GJ, Wang AHJ, Ughetto G, van der Marel G, van Boom JH, Rich A. Proc Natl Acad Sci USA, 1980, 77: 7204–7208

    Article  CAS  Google Scholar 

  56. Li M, Liu L, Xiao X, Xi N, Wang Y. Sci China Mater, 2017, 60: 269–278

    Article  Google Scholar 

  57. Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC. Nature, 1998, 391: 806–811

    Article  CAS  Google Scholar 

  58. Timmons L, Fire A. Nature, 1998, 395: 854–854

    Article  CAS  Google Scholar 

  59. Montgomery MK, Xu S, Fire A. Proc Natl Acad Sci USA, 1998, 95: 15502–15507

    Article  CAS  Google Scholar 

  60. Hormeño S, Ibarra B, Carrascosa JL, Valpuesta JM, Moreno-Herrero F, Arias-Gonzalez JR. BioPhys J, 2011, 100: 1996–2005

    Article  Google Scholar 

  61. Hormeño S, Moreno-Herrero F, Ibarra B, Carrascosa JL, Valpuesta JM, Arias-Gonzalez JR. BioPhys J, 2011, 100: 2006–2015

    Article  Google Scholar 

  62. Hormeño S, Ibarra B, Valpuesta JM, Carrascosa JL, Ricardo Arias-Gonzalez J. Biopolymers, 2012, 97: 199–208

    Article  Google Scholar 

  63. Herrero-Galán E, Fuentes-Perez ME, Carrasco C, Valpuesta JM, Carrascosa JL, Moreno-Herrero F, Arias-Gonzalez JR. J Am Chem Soc, 2013, 135: 122–131

    Article  Google Scholar 

  64. Pyne A, Thompson R, Leung C, Roy D, Hoogenboom BW. Small, 2014, 10: 3257–3261

    Article  CAS  Google Scholar 

  65. Ares P, Fuentes-Perez ME, Herrero-Galán E, Valpuesta JM, Gil A, Gomez-Herrero J, Moreno-Herrero F. Nanoscale, 2016, 8: 11818–11826

    Article  CAS  Google Scholar 

  66. Schön P. Methods, 2016, 103: 25–33

    Article  Google Scholar 

  67. Zhang Y, Chen S, Ouyang Z, Hu J, Xiong Q, Li B, Huang Y, Li M, Jin C. Chin Sci Bull, 2000, 45: 1365–1368

    Article  CAS  Google Scholar 

  68. Chan TF, Ha C, Phong A, Cai D, Wan E, Leung L, Kwok PY, Xiao M. Nucleic Acids Res, 2006, 34: e113–e113

    Google Scholar 

  69. Neupane GP, Dhakal KP, Kim MS, Lee H, Guthold M, Joseph VS, Hong JD, Kim J. J Biomed Opt, 2014, 19: 051210

    Article  Google Scholar 

  70. Kim N, Kim HJ, Kim Y, Min KS, Kim SK. Anal Bioanal Chem, 2016, 408: 6453–6459

    Article  CAS  Google Scholar 

  71. Sørensen KT, Lopacinska JM, Tommerup N, Silahtaroglu A, Kristensen A, Marie R. Rev Sci Instrum, 2015, 86: 063702

    Article  Google Scholar 

  72. Rems L, Kawale D, Lee LJ, Boukany PE. Biomicrofluidics, 2016, 10: 043403

    Article  Google Scholar 

  73. Gross P, Laurens N, Oddershede LB, Bockelmann U, Peterman EJG, Wuite GJL. Nat Phys, 2011, 7: 731–736

    Article  CAS  Google Scholar 

  74. Candelli A, Wuite GJL, Peterman EJG. Phys Chem Chem Phys, 2011, 13: 7263–7272

    Article  CAS  Google Scholar 

  75. Suei S, Raudsepp A, Kent LM, Keen SAJ, Filichev VV, Williams MAK. Biochem BioPhys Res Commun, 2015, 466: 226–231

    Article  CAS  Google Scholar 

  76. Liu S, Chistol G, Bustamante C. BioPhys J, 2014, 106: 1844–1858

    Article  CAS  Google Scholar 

  77. Xu H, Li Q, Wang L, He Y, Shi J, Tang B, Fan C. Chem Soc Rev, 2014, 43: 2650–2661

    Article  CAS  Google Scholar 

  78. Baday M, Cravens A, Hastie A, Kim HJ, Kudeki DE, Kwok PY, Xiao M, Selvin PR. Nano Lett, 2012, 12: 3861–3866

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (21525523, 21574048, 21375042, 21405054), the National Basic Research Program of China (2015CB932600, 2013CB933000), the Special Fund for Strategic New Industry Development of Shenzhen, China (JCYJ20150616144425376), and 1000 Young Talent (to Fan Xia).

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Correspondence to Fan Xia.

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Zhan, S., Lou, X. & Xia, F. Recent advances in optical-based and force-based single nucleic acid imaging. Sci. China Chem. 60, 1267–1276 (2017). https://doi.org/10.1007/s11426-017-9097-4

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